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- PDB-5k8r: Structure of human clustered protocadherin gamma B3 EC1-4 -

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Basic information

Entry
Database: PDB / ID: 5k8r
TitleStructure of human clustered protocadherin gamma B3 EC1-4
ComponentsProtocadherin gamma-B3
KeywordsCELL ADHESION / clustered protocadherin / protocadherin
Function / homology
Function and homology information


homophilic cell adhesion via plasma membrane adhesion molecules / nervous system development / cell adhesion / calcium ion binding / plasma membrane
Similarity search - Function
Cadherin, C-terminal catenin-binding domain / Cadherin C-terminal cytoplasmic tail, catenin-binding region / Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / Cadherin, N-terminal / Cadherin-like / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. ...Cadherin, C-terminal catenin-binding domain / Cadherin C-terminal cytoplasmic tail, catenin-binding region / Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / Cadherin, N-terminal / Cadherin-like / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protocadherin gamma-B3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNicoludis, J.M. / Vogt, B.E. / Gaudet, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
CitationJournal: Elife / Year: 2016
Title: Antiparallel protocadherin homodimers use distinct affinity- and specificity-mediating regions in cadherin repeats 1-4.
Authors: Nicoludis, J.M. / Vogt, B.E. / Green, A.G. / Scharfe, C.P. / Marks, D.S. / Gaudet, R.
History
DepositionMay 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protocadherin gamma-B3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,55515
Polymers45,8001
Non-polymers75514
Water2,162120
1
A: Protocadherin gamma-B3
hetero molecules

A: Protocadherin gamma-B3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,11030
Polymers91,6002
Non-polymers1,51028
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5690 Å2
ΔGint-139 kcal/mol
Surface area43260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.881, 161.229, 53.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protocadherin gamma-B3 / PCDH-gamma-B3


Mass: 45800.051 Da / Num. of mol.: 1 / Fragment: UNP residues 31-444
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCDHGB3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5G1

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Non-polymers , 6 types, 134 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7 4% ethylene glycol 5% PEG500MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→47.35 Å / Num. obs: 19844 / % possible obs: 92 % / Redundancy: 6.8 % / Biso Wilson estimate: 37.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1334 / Net I/σ(I): 10.06
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.962 / Mean I/σ(I) obs: 0.98 / % possible all: 42

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Processing

Software
NameVersionClassification
PHENIXdev_2276refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zi9

4zi9


Resolution: 2.5→47.35 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.5
RfactorNum. reflection% reflection
Rfree0.2587 1814 9.96 %
Rwork0.2053 --
obs0.2106 18204 91.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3219 0 31 120 3370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063295
X-RAY DIFFRACTIONf_angle_d0.6184477
X-RAY DIFFRACTIONf_dihedral_angle_d14.0971240
X-RAY DIFFRACTIONf_chiral_restr0.052516
X-RAY DIFFRACTIONf_plane_restr0.005594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.56760.3147550.2604518X-RAY DIFFRACTION38
2.5676-2.64320.37111020.2898868X-RAY DIFFRACTION64
2.6432-2.72850.33531140.29221229X-RAY DIFFRACTION90
2.7285-2.8260.30841530.29231335X-RAY DIFFRACTION99
2.826-2.93920.29891560.27661359X-RAY DIFFRACTION100
2.9392-3.07290.3371500.27151335X-RAY DIFFRACTION100
3.0729-3.23490.33881520.23751389X-RAY DIFFRACTION100
3.2349-3.43750.25991490.21931358X-RAY DIFFRACTION100
3.4375-3.70280.25971520.20031352X-RAY DIFFRACTION100
3.7028-4.07530.21661540.17071379X-RAY DIFFRACTION100
4.0753-4.66460.19871570.14891389X-RAY DIFFRACTION100
4.6646-5.87550.22491560.16661401X-RAY DIFFRACTION100
5.8755-49.61280.2391640.18131478X-RAY DIFFRACTION100

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